Small RNA-mediated chromatin silencing directed to the 3' region of the Arabidopsis gene encoding the developmental regulator, FLC

Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3633-8. doi: 10.1073/pnas.0611459104. Epub 2007 Feb 20.


Small RNA-mediated chromatin silencing is well characterized for repeated sequences and transposons, but its role in regulating single-copy endogenous genes is unclear. We have identified two small RNAs (30 and 24 nucleotides) corresponding to the reverse strand 3' to the canonical poly(A) site of FLOWERING LOCUS C (FLC), an Arabidopsis gene encoding a repressor of flowering. Genome searches suggest that these RNAs originate from the FLC locus in a genomic region lacking repeats. The 24-nt small RNA, which is most abundant in developing fruits, is absent in mutants defective in RNA polymerase IVa, RNA-DEPENDENT RNA POLYMERASE 2, and DICER-LIKE 3, components required for RNAi-mediated chromatin silencing. The corresponding genomic region shows histone 3 lysine 9 dimethylation, which was reduced in a dcl2,3,4 triple mutant. Investigations into the origins of the small RNAs revealed a polymerase IVa-dependent spliced, antisense transcript covering the 3' FLC region. Mutation of this genomic region by T-DNA insertion led to FLC misexpression and delayed flowering, suggesting that RNAi-mediated chromatin modification is an important component of endogenous pathways that function to suppress FLC expression.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics*
  • Arabidopsis Proteins / genetics*
  • Arabidopsis Proteins / metabolism
  • Chromatin / genetics*
  • Chromatin Immunoprecipitation
  • DNA-Directed RNA Polymerases / genetics
  • DNA-Directed RNA Polymerases / metabolism
  • MADS Domain Proteins / genetics*
  • MADS Domain Proteins / metabolism
  • Mutation / genetics
  • RNA Interference*
  • RNA, Small Interfering / genetics*
  • RNA-Dependent RNA Polymerase / genetics
  • RNA-Dependent RNA Polymerase / metabolism
  • Reverse Transcriptase Polymerase Chain Reaction
  • Ribonuclease III / genetics
  • Ribonuclease III / metabolism


  • Arabidopsis Proteins
  • Chromatin
  • FLF protein, Arabidopsis
  • MADS Domain Proteins
  • RNA, Small Interfering
  • RNA polymerase IV, Arabidopsis
  • RNA-Dependent RNA Polymerase
  • DNA-Directed RNA Polymerases
  • DCL3 protein, Arabidopsis
  • Ribonuclease III